The oral cavity is continuous with the gastrointestinal tract and in children, oral health may be closely linked with the overall health of the GI tract. In the case of pediatric Crohn's disease (CD), oral manifestations are an important clinical indicator of intestinal disease. Recent studies of the microbiome in IBD suggest that translocation of oral microbes to the gut may be a common feature of the microbial dysbiosis which is a signature of both CD and ulcerative colitis (UC). Murine studies suggest that translocation of oral bacteria and yeasts to the lower GI tract may trigger inflammation in susceptible hosts, providing a mechanistic link to the development of IBD. Conversely, some studies have shown that dysbiosis of the oral microbiome may occur, possibly as a result of inflammatory responses and could represent a useful source of biomarkers of GI health. This review summarizes our current knowledge of the oral microbiome in IBD and presents current hypotheses on the potential role of this community in the pathogenesis of these diseases.

The oral microbiome was examined in a cohort of treatment naïve children diagnosed with Crohn’s disease (n=27, CD) or ulcerative colitis (n=6, UC). A cohort of 28 children were grouped as a healthy control (HC) group. Bacterial DNA was extracted from tongue and buccal swabs and the V1-V2 region of the 16s gene was amplified and sequenced using the MiSeq. Sequences were analysed with the Mothur pipeline.Reduced biodiversity of the tongue was indicated by differences in the inverse Simpson’s index for both sites (CD tongue=9.39; HC=12.87). Analysis of species richness by rarefaction showed a significant reduction in species richness in CD tongue samples compared to HC tongue samples. Analysis of community structure and membership using AMOVA showed that the populations on HC and CD tongues were significantly different (P <0.001). LEfSe analysis identified 20 OTUs that were significantly enriched on the tongues of healthy children including H. parainfluenzae, N. flavescens, F. periodonticum, Streptococcus sp., Porphyromonas sp., Actinomyces sp. Children with Crohn’s have an altered microflora that may contribute to their oral health problems. These data could potentially be used to diagnose a patients overall gastrointestinal health.

Background There is a limited literature describing the oral microbiome and its diagnostic potential in paediatric inflammatory bowel disease (IBD). Methods We examined the dorsum tongue microbiome by V1-V2 sequencing in a cohort of 156 treatment naïve children diagnosed with IBD compared to 102 healthy control children. Microbiome changes over time following treatment were examined in a subset of patients and associations between IBD diagnosis and dysbiosis were explored. Results Analysis of community structure of the microbiome in tongue samples revealed that IBD samples significantly diverged from healthy control samples (PERMANOVA P=0.0009) and exhibited a reduced abundance of Clostridia in addition to several major oral genera (Veillonella, Prevotella, Fusobacterium species) with an increased abundance of streptococci. This dysbiosis was more marked in patients with severe disease. Higher levels of the potential pathobionts Klebsiella and Pseudomonas spp. were also associated with IBD. In terms of predicted functions, the IBD oral microbiome was potentially more acidogenic and exhibited reduced capacity for B vitamin biosynthesis. We used a machine learning approach to develop a predictive model of IBD which exhibited a mean-prediction AUC: 0.762. Finally, we examined a subset of 53 patients following 12 months of therapy and could show resolution of oral dysbiosis demonstrated by a shift towards a healthy community structure and a significant reduction in oral dysbiosis. Conclusion Oral dysbiosis found in children with IBD is disease severity related and resolves over time following successful IBD treatment.